Understanding the Significance and Implications of Antibody Numbering and Antigen-Binding Surface/Residue Definition.

Marylène S Vandevenne,Serge Muyldermans,Eric Sauvage,Birgit Quinting,Moreno Galleni,Patrice Filée,Mathieu Dondelinger

doi:10.3389/fimmu.2018.02278

Abstract

Monoclonal antibodies are playing an increasing role in both human and animal health. Different strategies of protein and chemical engineering, including humanization techniques of non-human antibodies were applied successfully to optimize clinical performances of antibodies. Despite the emergence of techniques allowing the development of fully human antibodies such as transgenic Xeno-mice, antibody humanization remains a standard procedure for therapeutic antibodies. An important prerequisite for antibody humanization requires standardized numbering methods to define precisely complementary determining regions (CDR), frameworks and residues from the light and heavy chains that affect the binding affinity and/or specificity of the antibody-antigen interaction. The recently generated deep-sequencing data and the increasing number of solved three-dimensional structures of antibodies from human and non-human origins have led to the emergence of numerous databases. However, these different databases use different numbering conventions and CDR definitions. In addition, the large fluctuation of the variable chain lengths, especially in CDR3 of heavy chains (CDRH3), hardly complicates the comparison and analysis of antibody sequences and the identification of the antigen binding residues. This review compares and discusses the different numbering schemes and “CDR” definition that were established up to date. Furthermore, it summarizes concepts and strategies used for numbering residues of antibodies and CDR residues identification. Finally, it discusses the importance of specific sets of residues in the binding affinity and/or specificity of immunoglobulins.

Highlights

In 1986, Muromonab-CD3 was the first monoclonal antibody approved as a drug for human therapy
As shown earlier, the Kabat complementary determining regions (CDR) definitions are based on sequence alignments while the Chothia CDR definition better reflects the loop structure in antibodies’ 3D architecture
The binding of the two complementary surfaces is mostly driven by aromatic residues that establish van der Waals and hydrophobic interactions while the strengthening of the complex involves rather electrostatic interactions and hydrogen bonds established between side chains of adequately positioned charged and polar residues

Summary

INTRODUCTION

In 1986, Muromonab-CD3 was the first monoclonal antibody (mAb) approved as a drug for human therapy. As shown earlier, the Kabat (and IMGT) CDR definitions are based on sequence alignments while the Chothia CDR definition better reflects the loop structure in antibodies’ 3D architecture This lack of agreement in defining precisely the CDR lengths and positions is somehow unexpected since these regions were shown to be responsible for the antigen-binding activity already a long time ago [16]. In 2010, Abhinandan and Martin made a more comprehensive analysis of the diversity between VH and VL packing angles including 567 antibody crystal structures They developed a method to predict the packing/orientation of the heavy and light chain variable domains based on the presence of specific amino acids located at the interface between these two domains. Using right triangle simple trigonometry and assuming a variable region length of 37 Å, a difference of 1◦ between the VL/VH domains causes a displacement of

Findings

DISCUSSION

CONCLUSION